Pinnatoxin H was isolated from a culture of the dinoflagellate Vulcanodinium rugosum isolated from the South China Sea. The structure of pinnatoxin H was elucidated by LC–MS/MS and NMR spectroscopy. It was found to have the same macrocyclic structure and substituents as pinnatoxins D, E and F, but the side chain on the cyclohexenyl ring was an ethenyl group, as found in pinnatoxin G and portimine. The observation that this strain of V. rugosum produced only pinnatoxin H and portimine is consistent with previous findings that the profile of pinnatoxins can vary significantly among strains. The acute toxicity of pinnatoxin H to mice was 67 μg/kg (intraperitoneal) and 163 μg/kg (gavage).